The Effects of Permafrost Thaw on Soil Hydrologic, Thermal, and Carbon Dynamics in an Alaskan Peatland

Recent warming at high-latitudes has accelerated permafrost thaw in northern peatlands, and thaw can have profound effects on local hydrology and ecosystem carbon balance. To assess the impact of permafrost thaw on soil organic carbon (OC) dynamics, we measured soil hydrologic and thermal dynamics and soil OC stocks across a collapse-scar bog chronosequence in interior Alaska. We observed dramatic changes in the distribution of soil water associated with thawing of ice-rich frozen peat. The impoundment of warm water in collapse-scar bogs initiated talik formation and the lateral expansion of bogs over time. On average, Permafrost Plateaus stored 137 ± 37 kg C m⁻², whereas OC storage in Young Bogs and Old Bogs averaged 84 ± 13 kg C m⁻². Based on our reconstructions, the accumulation of OC in near-surface bog peat continued for nearly 1,000 years following permafrost thaw, at which point accumulation rates slowed. Rapid decomposition of thawed forest peat reduced deep OC stocks by nearly half during the first 100 years following thaw. Using a simple mass-balance model, we show that accumulation rates at the bog surface were not sufficient to balance deep OC losses, resulting in a net loss of OC from the entire peat column. An uncertainty analysis also revealed that the magnitude and timing of soil OC loss from thawed forest peat depends substantially on variation in OC input rates to bog peat and variation in decay constants for shallow and deep OC stocks. These findings suggest that permafrost thaw and the subsequent release of OC from thawed peat will likely reduce the strength of northern permafrost-affected peatlands as a carbon dioxide sink, and consequently, will likely accelerate rates of atmospheric warming.     

Mechanism of inhibition of retrovirus release from cells by interferon-induced gene ISG15

Budding of retroviruses from cell membranes requires ubiquitination of Gag and recruitment of cellular proteins involved in endosome sorting, including endosome sorting complex required for transport III (ESCRT-III) protein complex and vacuolar protein sorting 4 (VPS4) and its ATPase. In response to infection, a cellular mechanism has evolved that blocks virus replication early and late in the budding process through expression of interferon-stimulated gene 15 (ISG15), a dimer homologue of ubiquitin. Interferon treatment of DF-1 cells blocks avian sarcoma/leukosis virus release, demonstrating that this mechanism is functional under physiological conditions. The late block to release is caused in part by a loss in interaction between VPS4 and its coactivator protein LIP5, which is required to promote the formation of the ESCRT III-VPS4 double-hexamer complex to activate its ATPase. ISG15 is conjugated to two different LIP5-ESCRT-III-binding charged multivesicular body proteins, CHMP2A and CHMP5. Upon ISGylation of each, interaction with LIP5 is no longer detected. Two other ESCRT-III proteins, CHMP4B and CHMP6, are also conjugated to ISG15. ISGylation of CHMP2A, CHMP4B, and CHMP6 weakens their binding directly to VPS4, thereby facilitating the release of this protein from the membrane into the cytosol. The remaining budding complex fails to release particles from the cell membrane. Introducing a mutant of ISG15 into cells that cannot be conjugated to proteins prevents the ISG15-dependent mechanism from blocking virus release. CHMP5 is the primary switch to initiate the antiviral mechanism, because removal of CHMP5 from cells prevents ISGylation of CHMP2A and CHMP6.     

pHG165: A pBR322 copy number derivative of pUC8 for cloning and expression

During the construction of the Messing pUC plasmid series, the rop(rom) gene of pBR322 which mediates the activity of RNAI was deleted. This has resulted in an elevated copy number for the pUC plasmids which makes the expression of beta-galactosidase activity constitutive in a host containing the Iqtss lac repressor. We describe the construction of a new series of vectors which retain the pUC multiple cloning site (MCS) but in which copy number control has been recovered. In addition, the lac alpha/lac promoter expression region has been inserted into a HpaI cassette. This facilitates the movement of recombinant DNA clones within the MCS. It also increases the complementation activity of the lac alpha peptide by an order of magnitude, allowing selection of recombinants by their Lac- phenotype on MacConkey agar.     

Phosphorylation of the Pseudomonas aeruginosa response regulator AlgR is essential for type IV fimbria-mediated twitching motility

The response regulator AlgR is required for both alginate biosynthesis and type IV fimbria-mediated twitching motility in Pseudomonas aeruginosa. In this study, the roles of AlgR signal transduction and phosphorylation in twitching motility and biofilm formation were examined. The predicted phosphorylation site of AlgR (aspartate 54) and a second aspartate (aspartate 85) in the receiver domain of AlgR were mutated to asparagine, and mutant algR alleles were introduced into the chromosome of P. aeruginosa strains PAK and PAO1. Assays of these mutants demonstrated that aspartate 54 but not aspartate 85 of AlgR is required for twitching motility and biofilm initiation. However, strains expressing AlgR D85N were found to be hyperfimbriate, indicating that both aspartate 54 and aspartate 85 are involved in fimbrial biogenesis and function. algD mutants were observed to have wild-type twitching motility, indicating that AlgR control of twitching motility is not mediated via its role in the control of alginate biosynthesis. In vitro phosphorylation assays showed that AlgR D54N is not phosphorylated by the enteric histidine kinase CheA. These findings indicate that phosphorylation of AlgR most likely occurs at aspartate 54 and that aspartate 54 and aspartate 85 of AlgR are required for the control of the molecular events governing fimbrial biogenesis, twitching motility, and biofilm formation in P. aeruginosa.     

Development of a seed DNA-based genotyping system for marker-assisted selection in maize

Leaf collection from the field, labeling and tracking back to the source plants after genotyping are rate limiting steps in leaf DNA-based genotyping. In this study, an optimized genotyping method using endosperm DNA sampled from single maize seeds was developed, which can be used to replace leaf DNA-based genotyping for both genetic studies and breeding applications. A similar approach is likely to be suitable for all plants with relatively large seeds. Part of the endosperm was excised from imbibed maize seeds and DNA extracted in 96-tube plates using individuals from eight F₂ populations and seven inbreds. The quality of the resultant DNA was functionally comparable to DNA extracted from leaf tissue. Extraction from 30 mg of endosperm yields 3–10 μg DNA, which is sufficient for analysis of 200–400 agarose-gel PCR-based markers, with the potential for several million chip-based SNP marker analyses. By comparing endosperm DNA and leaf DNA for individuals from an F₂ population, genotyping errors caused by pericarp contamination and hetero-fertilization were found to average 3.8 and 0.6%, respectively. Endosperm sampling did not affect germination rates under controlled conditions, although under normal field conditions the germination rate, seedling establishment, and growth vigor were significantly lower than that of non-sampled controls for some genotypes. However, careful field management can compensate for these effects. Seed DNA-based genotyping lowered costs by 24.6% compared to leaf DNA-based genotyping due to reduced field plantings and labor costs. A substantial advantage of this approach is that it can be used to select desirable genotypes before planting. As such it provides an opportunity for dramatic improvements in the efficiency and selective gain of breeding systems based on optimum combinations of marker-assisted selection and phenotypic selection within and between generations.     

Volume changes of Commelina communis guard cell protoplasts in response to K+, light and CO2

The effects of K⁺ concentration, light intensity and CO₂ levels on the volume of Commelina communis L. guard cell protoplasts were studied. Two degrees of swelling response were observed, both dependent on an external supply of K⁺, but not necessarily on the supply of a permeant anion. The presence of K⁺ itself, independent of light or CO₂ level, stimulated swelling at a relatively slow rate. When K⁺, light and low CO₂ conditions were supplied together, the swelling was relatively rapid and of high magnitude. The rapid swelling was specific for K⁺ and Rb⁺ giving a half maximal effect after 2 h at a KCl concentration of about 18 mmol m⁻³. The addition of CaCl₂ at 1 mol m⁻³ inhibited K⁺-dependent swelling under all conditions tested. The response to light and low CO₂ levels by Commelina guard cell protoplasts is thought to reflect a high degree of physiological integrity.     

A half a century of measuring ungulate body condition using indices: is it time for a change?

From a literature review of five wildlife ecology journals since 1937, we document how using indices to monitor ungulate body condition is common practice, with the kidney fat index (KFI = weight of fat around the kidneys/weight of kidneys without fat × 100) as the favoured tool (82% of studies). In this context, we highlight the problems of using indices when underlying statistical assumptions are not met (isometry, parallel slopes between treatments). We show, with real and simulated data for two cervids with contrasting fat storage strategies, how results from analysis of variance of KFI values differ from analysis of covariance (ANCOVA) of raw data. We conclude that the KFI is affected by the restrictions typically associated with derived index values, and as a consequence, statistical analysis of the KFI could generate spurious results leading to erroneous interpretations concerning variation in body condition of ungulate populations. Thus, we recommend analysing fat weight as an untransformed variable in ANCOVA (kidney weight as covariate) to describe body condition variation in ungulates. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Coating and selective deposition of nanofilm on silicone rubber for cell adhesion and growth

A recently developed method for surface modification, layer-by-layer (LbL) assembly, has been applied to silicone, and its ability to encourage endothelial cell growth and control cell growth patterns has been examined. The surfaces studied consisted of a precursor, with alternating cationic polyethyleneimine (PEI) and anionic sodium polystyrene sulfonate (PSS) layers followed by alternating gelatin and poly-d-lysine (PDL) layers. Film growth increased linearly with the number of layers. Each PSS/PEI bilayer was 3 nm thick, and each gelatin/PDL bilayer was 5 nm thick. All layers were more hydrophilic than the unmodified silicone rubber surface, as determined from contact angle measurements. The contact angle was primarily dictated by the outermost layer. Of the coatings studied, gelatin was the most hydrophilic. A film of (PSS/PEI)₄/(gelatin/PDL)₄/ gelatin was highly favorable for cell adhesion and growth, in contrast to films of (PSS/PEI)₈ or (PSS/PEI)₈/PSS. Cell growth patterns were successfully controlled by selective deposition of microspheres on silicone rubber, using microcontact printing with a silicone stamp. Cell adhesion was confined to the region of microsphere deposition. These results demonstrate that the LbL self-assembly technique provides a general approach to coat and selectively deposit films with nanometer thickness on silicone rubber. Furthermore, they show that this method is a viable technique for controlling cellular adhesion and growth.     

Power and phase properties of oscillatory neural responses in the presence of background activity

Natural sensory inputs, such as speech and music, are often rhythmic. Recent studies have consistently demonstrated that these rhythmic stimuli cause the phase of oscillatory, i.e. rhythmic, neural activity, recorded as local field potential (LFP), electroencephalography (EEG) or magnetoencephalography (MEG), to synchronize with the stimulus. This phase synchronization, when not accompanied by any increase of response power, has been hypothesized to be the result of phase resetting of ongoing, spontaneous, neural oscillations measurable by LFP, EEG, or MEG. In this article, however, we argue that this same phenomenon can be easily explained without any phase resetting, and where the stimulus-synchronized activity is generated independently of background neural oscillations. It is demonstrated with a simple (but general) stochastic model that, purely due to statistical properties, phase synchronization, as measured by ‘inter-trial phase coherence’, is much more sensitive to stimulus-synchronized neural activity than is power. These results question the usefulness of analyzing the power and phase of stimulus-synchronized activity as separate and complementary measures; particularly in the case of attempting to demonstrate whether stimulus-synchronized neural activity is generated by phase resetting of ongoing neural oscillations.